Silence greeted the players as they lined up to sing their national anthems at Estadio Beira-Rio, before the officials urged them to skip the formality and engage in the pre-match handshakes instead.
France went on to win the match 3-0 over 10-man Honduras, with Karim Benzema scoring either side of a Noel Valladares own goal, but FIFA have now issued an apology for the incident and vowed to get to the bottom of the problem.
In a message sent to the Honduran Football Federation, secretary general Jerome Valcke said: "I would like to offer you the most sincere apologies from FIFA regarding the technical incident which prevented the national anthems of France and Honduras from being played in Porto Alegre, as established by the protocol for all the matches between national teams carried out within the framework of FIFA."
Valcke went on to stress that respect is an integral part of the FIFA protocol for matches and that the teams involved would be kept updated on the outcome of the investigation into the matter.
Honduras face Ecuador in their next Group E fixture on Friday, while leading duo France and Switzerland meet in Salvador.
